crossing96/oncoscreening huggingface dataset:
Nomograms including the UBC(®) Rapid test to detect primary bladder cancer based on a multicentre dataset.	OBJECTIVES: To evaluate the clinical utility of the urinary bladder cancer antigen test UBC(®) Rapid for the diagnosis of bladder cancer (BC) and to develop and validate nomograms to identify patients at high risk of primary BC. PATIENTS AND METHODS: Data from 1787 patients from 13 participating centres, who were tested between 2012 and 2020, including 763 patients with BC, were analysed. Urine samples were analysed with the UBC(®) Rapid test. The nomograms were developed using data from 320 patients and externally validated using data from 274 patients. The diagnostic accuracy of the UBC(®) Rapid test was evaluated using receiver-operating characteristic curve analysis. Brier scores and calibration curves were chosen for the validation. Biopsy-proven BC was predicted using multivariate logistic regression. RESULTS: The sensitivity, specificity, and area under the curve for the UBC(®) Rapid test were 46.4%, 75.5% and 0.61 (95% confidence interval [CI] 0.58-0.64) for low-grade (LG) BC, and 70.5%, 75.5% and 0.73 (95% CI 0.70-0.76) for high-grade (HG) BC, respectively. Age, UBC(®) Rapid test results, smoking status and haematuria were identified as independent predictors of primary BC. After external validation, nomograms based on these predictors resulted in areas under the curve of 0.79 (95% CI 0.72-0.87) and 0.95 (95% CI: 0.92-0.98) for predicting LG-BC and HG-BC, respectively, showing excellent calibration associated with a higher net benefit than the UBC(®) Rapid test alone for low and medium risk levels in decision curve analysis. The R Shiny app allows the results to be explored interactively and can be accessed at www.blucab-index.net. CONCLUSION: The UBC(®) Rapid test alone has limited clinical utility for predicting the presence of BC. However, its combined use with BC risk factors including age, smoking status and haematuria provides a fast, highly accurate and non-invasive tool for screening patients for primary LG-BC and especially primary HG-BC.	bladder
Comprehensive Analysis Identified ETV7 as a Potential Prognostic Biomarker in Bladder Cancer.	BACKGROUND: The tumor microenvironment (TME) plays a crucial role in the initiation and progression of cancer. Bladder cancer (BLCA) is a malignant tumor of the genitourinary system. Its heterogeneity results in significant differences in the prognosis of patients. To date, this is still a huge challenge for clinical treatment. In recent years, more and more evidence showed that dysregulation of transcription factors (TFs) plays an important role in tumor progression, invasion, and metastasis. Unfortunately, the role of TFs on the tumor microenvironment in bladder cancer is unclear. METHODS: The original data of BLCA and corresponding adjacent tissues were obtained from The Cancer Genome Atlas (TCGA) database. TFs were downloaded from the Animal Transcription Factor DataBase (Animal TFDB). Intersection analysis was used to obtain TFs that were differentially expressed between tumor and adjacent tissues. Gene Set Cancer Analysis (GSCALite) and CIBERSORT software were used to reveal the key differentially expressed TFs (DE-TFs). Subsequently, UALCAN and Human Protein Atlas (HPA) databases were used to disclose the expression of key DE-TFs in BLCA. The K-M curve divulged the relationship between the key DE-TFs and the patient's overall survival (OS), and the univariate and multivariate Cox regression analyses were conducted to explore independent prognostic factors. The cluster profiler package and Gene Set Enrichment Analysis (GSEA) were used for functional enrichment of genes related to the key DE-TFs. Finally, CIBERSORT software analyzed the immune landscape of BLCA. RESULTS: We obtained a total of 117 BLCA-related DE-TFs. Among them, ETV7 was identified as the key DE-TFs due to its association with the autophagy activation pathway and various immune cells in cancer. Online databases of UALCAN and HPA indicated that ETV7 was overexpressed in tumors and negatively correlated with tumor severity. The K-M curve showed that the OS of patients with high expression of ETV7 was poor, which indicated that it was an independent prognostic factor. Functional enrichment of 87 DEGs between ETV7-high and -low expression groups indicated that it was closely related to the immune response and the functions of a variety of immune cells. Finally, CIBERSORT results proved that the high and low expression of ETV7 also caused significant differences in the tumor immune microenvironment of patients. CONCLUSION: Overall, we proved that the transcription factor ETV7 was a novel prognostic factor, which may improve the individualized outcome prediction in BLCA by regulating the tumor immune microenvironment.	bladder
Evaluation of PD-1 and PD-L1 expression in canine urothelial carcinoma cell lines.	Urothelial carcinoma (UC) is the most common urinary tumor in dogs and despite combinational therapies, only modest improvements in survival have been achieved in recent years. Given the utility of monoclonal antibodies against PD-1 and PD-L1 in human UC, we evaluated the protein and mRNA expression in three established canine urothelial carcinoma cell lines. Flow cytometry and western blot analysis confirmed cell line expression of both molecules in varying degrees. Reverse transcription PCR (RT-PCR) documented mRNA expression in all three cell lines for both PD-1 and PD-L1. Fluorescence microscopy was consistent with strong PD-1 and PD-L1 expression in the canine cell lines and was in line with previous human literature. Importantly, the flow cytometry work described in this study revealed higher cell intrinsic PD-1 expression in these cell lines which may have implications for tumor behavior and potential treatment opportunities in the future. Further work is necessary to determine the expression patterns in canine UC and potential for benefit with immunotherapy directed against PD-1 and PD-L1.	bladder
Extraperitonealization of ileal conduit reduces parastomal hernia after cystectomy and ileal conduit diversion.	OBJECTIVE: Parastomal hernia (PSH) is a common complication of ileal conduit diversion after radical cystectomy. Novel surgical techniques for preventing PSH formation are needed. We aimed to evaluate surgical technique of extraperitonealizing the ileal conduit (modified ileal conduit) for preventing PSH. METHODS: A retrospective analysis of 375 consecutive patients who underwent ileal conduit after cystectomy at the Sun Yat-sen University Cancer Center between January 1, 2000 and June 31, 2019 was conducted. 214 patients had modified ileal conduit diversion and 161 patients conventional ileal conduit (Bricker) diversion. The demographic and clinicopathologic characteristics of patients in the 2 groups were compared using the t test and Chi square test. Univariable and multivariable Cox regression analyses were used to predict the risk of PSH formation. RESULTS: The 2 groups were comparable in regard to all demographic and clinicopathologic variables. The incidence of PSH diagnosed by CT scan was 7.5% in the modified group and 21.1% in the conventional group (P < 0.001). High BMI and history of prior abdominal surgery was identified by univariable analysis as risk factors of PSH formation. Multivariable analyses revealed that technique of extraperitonealizing ileal conduit significantly reduced incidence of PSH in patients with or without risk factors of PSH formation (OR = 0.29, 95% CI 0.16-0.54, P < 0.001). CONCLUSIONS: Technique of extraperitonealizing ileal conduit appeared to be effective in reducing PSH formation after ileal conduit diversion.	bladder
Comparison of the diagnostic accuracy and validity of biparametric MRI and multiparametric MRI-based VI-RADS scoring in bladder cancer; is contrast material really necessary in detecting muscle invasion?	PURPOSE: (1) To evaluate the accuracy and validity of the biparametric MRI (bp-MRI), including T2-weigthed image (WI) and DWI sequences, and the availability of an alternative to the multiparametric MRI (mp-MRI), for the muscle-invasiveness assessment of bladder cancer (BC). (2) To evaluate the diagnostic performance and agreement of readers with different experiences in the abdominal imaging of using both protocols. METHODS: Preoperative bladder mp-MRI was performed on 128 patients with a initial diagnosis of BC. Two sets of images, set 1 (bp-MRI) and set 2 (mp-MRI), were independently evaluated by both readers. Descriptive statistics, including sensitivity, specificity, accuracy, and area under the curve (AUC), for VI-RADS scores were calculated using ≥ 4 as the cutoff for muscle invasion for each reader and image sets. Inter-reader agreement was evaluated using the Cohen's kappa coefficient. RESULTS: The sensitivity ranged between 90.3-93.5% and 87.1-90.3%, specificity ranged between 96.6-99.1% and 91.6-96.6%, accuracy ranged between 96-97.3% and 91.3-94.6%, and AUC ranged between 0.947-0.951 and 0.919-0.921, for bp-MRI and mp-MRI, and reader 1 and reader 2, respectively. No significant differences were shown in diagnostic performance for either reader between both the protocols (p = 0.238 and 0.318). There was excellent agreement among the readers in the VI-RADS scores, using both protocols. CONCLUSION: A bp-MRI protocol has a diagnostic accuracy comparable to an mp-MRI protocol for the detection of muscle-invasive BC using the VI-RADS criteria. Also, in both MRI protocols, the reader's experience does not appear to significantly affect diagnostic performance when using the VI-RADS criteria.	bladder
Association of Health-Care System and Survival in African American and Non-Hispanic White Patients With Bladder Cancer.	BACKGROUND: African American patients with bladder cancer have inferior outcomes compared with non-Hispanic White (White) patients. We hypothesize that access to health care is a primary determinant of this disparity. We compared outcomes by race for patients with bladder cancer receiving care within the predominant hybrid-payer health-care model of the United States captured in the Surveillance, Epidemiology, and End Results (SEER) database with those receiving care within the equal-access model of the Veterans' Health Administration (VHA). METHODS: African American and White patients diagnosed with bladder cancer were identified in SEER and VHA. Stage at presentation, bladder cancer-specific mortality (BCM), and overall survival (OS) were compared by race within each health-care system. RESULTS: The SEER cohort included 122 449 patients (93.7% White, 6.3% African American). The VHA cohort included 36 322 patients (91.0% White, 9.0% African American). In both cohorts, African American patients were more likely to present with muscle-invasive disease and metastases, but the differences between races were statistically significantly smaller in VHA. In SEER multivariable models, African American patients had worse BCM (hazard ratio [HR] = 1.22, 95% confidence interval [CI] = 1.15 to 1.29) and OS (HR = 1.26, 95% CI = 1.20 to 1.31). In contrast within the VHA, African American patients had similar BCM (HR = 0.97, 95% CI = 0.88 to 1.07) and OS (HR = 0.99, 95% CI = 0.93 to 1.05). CONCLUSIONS: In this study of contrasting health-care models, receiving medical care in an equal-access system was associated with reduced differences in stage at presentation and eliminated disparities in survival outcomes for African American patients with bladder cancer. Our findings highlight the importance of reducing financial barriers to care to notably improve health equity and oncologic outcomes for African American patients.	bladder
Durability of Response to Primary Chemoablation of Low-Grade Upper Tract Urothelial Carcinoma Using UGN-101, a Mitomycin-Containing Reverse Thermal Gel: OLYMPUS Trial Final Report.	PURPOSE: Our goal was to evaluate long-term safety and durability of response to UGN-101, a mitomycin-containing reverse thermal gel, as primary chemoablative treatment for low-grade upper tract urothelial carcinoma. MATERIALS AND METHODS: In this open-label, single-arm, multicenter, phase 3 trial (NCT02793128), patients ≥18 years of age with primary or recurrent biopsy-proven low-grade upper tract urothelial carcinoma received 6 once-weekly instillations of UGN-101 via retrograde catheter to the renal pelvis and calyces. Those with complete response (defined as negative ureteroscopic evaluation, negative cytology and negative for-cause biopsy) 4-6 weeks after the last instillation were eligible for up to 11 monthly maintenance instillations and were followed for ≥12 months with quarterly evaluation of response durability. Durability of complete response was determined by ureteroscopic evaluation; duration of response was estimated by the Kaplan-Meier method. Treatment-emergent adverse events (TEAEs) were monitored. RESULTS: Of 71 patients who initiated treatment, 41 (58%) had complete response to induction therapy and consented to long-term followup; 23/41 patients (56%) remained in complete response after 12 months (95% CI 40, 72), comprising 6/12 (50%) who did not receive any maintenance instillations and 17/29 (59%) who received ≥1 maintenance instillation. Kaplan-Meier analysis of durability was estimated as 82% (95% CI 66, 91) at 12 months. Ureteric stenosis was the most frequently reported TEAE (31/71, 44%); an increasing number of instillations appeared to be associated with increased incidence of urinary TEAEs. CONCLUSIONS: Durability of response to UGN-101 with or without maintenance treatment is clinically meaningful, offering a kidney-sparing therapeutic alternative for patients with low-grade disease.	bladder
A Nomogram Model to Predict Recurrence of Non-Muscle Invasive Bladder Urothelial Carcinoma After Resection Based on Clinical Parameters and Immunohistochemical Markers.	OBJECTIVE: This study aims to establish a nomogram model by combining traditional clinical parameters with immunohistochemical markers to predict the recurrence of non-muscle invasive bladder urothelial carcinoma (NMIBUC) after resection. METHODS: In total, 504 patients were included in this study. Of these patients, 353 underwent transurethral resection of bladder tumor (TURBT) in the Yongchuan Hospital of Chongqing Medical University and were identified as a training cohort. Univariate and multivariate Cox regression analyses were used to determine the risk factors associated with recurrence in the training cohort and to establish a nomogram model. A total of 151 patients who were hospitalized in the Second Affiliated Hospital of Chongqing Medical University (validation cohort) were used for further validation. The calibration curve was generated for internal and external model validation. The clinical practicability of this model was further verified by comparing the consistency index (C-index) among various models. RESULTS: The mean follow-up time of the training cohort was 45.6 months (range 4-90). In total, 146 patients relapsed in training cohort. After univariate analysis, multivariate analysis further confirmed tumor grade (p=.034), immediate postoperative instillation therapy (p=.025), Ki67 (p=.047), P53 (p=.038) and CK20 (p=.049) as independent risk factors for recurrence, and these factors were included in the nomogram model. The model more accurately predicted recurrence compared with other models based on the highest C-index of 0.82 (95% CI, 0.78-0.86) in the training cohort and 0.80 (95% CI, 0.77-0.83) in the validation cohort. CONCLUSIONS: This proposed nomogram model based on traditional clinical parameters and immunohistochemical markers can more accurately predict postoperative recurrence in patients with NMIBUC.	bladder
Incidence, mortality and survival of bladder neoplasms in the Czech Republic in the period 1977-2017: a time trend analysis.	BACKGROUND: Bladder neoplasms represent a significant disease burden in the Czech population. This study aimed to perform a complex time trend analysis of incidence, mortality, and survival of 76,505 patients with bladder neoplasms based on the Czech National Cancer Registry for 1977-2017. MATERIALS AND METHODS: The time trends of incidence and mortality were evaluated using the joinpoint regression. The relative survival and Cox proportional hazards model were used for survival analysis. RESULTS: After 2004, a significant annual decrease by 1.9% in the incidence of malignant tumors of the bladder (C67) was observed, accompanied by a sharp annual increase in the incidence of in situ bladder cancer (D090) by 16.9%. For mortality from malignant tumors of the bladder, a significant decrease by 1.4% annually was detected after 1998. The decline in both incidence and mortality was most pronounced in the below-65 years age group and in patients with a localized stage at dia-gnosis. While a significant decline in both incidence and mortality was observed for the first primary malignant tumors of the bladder, both these measures increased for malignant tumors of the bladder as subsequent primary neoplasms. The five-year relative survival of patients with malignant tumors of the bladder increased from 52.1% in 1990-1993 to 62.3% in 2013-2017. However, comparing the periods 2003-2007 and 2013-2017, a decrease has been observed. CONCLUSION: The decrease in the incidence and survival of malignant tumors of the bladder in the recent period is in particular caused by improved detection of in situ bladder cancer and classification changes. Other reasons for the decreasing survival include the increasing age at dia-gnosis, the growing number of subsequent primary neoplasms, and the increasing proportion of smokers among patients.	bladder
TRIM38 triggers the uniquitination and degradation of glucose transporter type 1 (GLUT1) to restrict tumor progression in bladder cancer.	BACKGROUND: Loss-of-function mutations or abnormal expressions of E ubiquitin ligases contributes to tumorigenesis. TRIM38 was reported to regulate immunity, inflammatory responses or apoptosis, but its roles in tumor progression remain inconclusive. This study aimed to investigate the functional roles of TRIM38 in bladder cancer to identify effective targets. METHODS: Firstly, the expression data of ubiquitination-associated genes were derived from the TCGA-BLCA cohort. Univariate Cox regression method was utilized to screen prognostic genes. Colony formation assay, Transwell assay, sphere formation assays were used to assess functional roles of TRIM38. TAP/MS assay was used to identify downstream substrates of TRIM38. Fresh clinical BLCA tissues were collected to evaluate the clinicopathological features of patients with different TRIM38 expression. The subcutaneous tumor models were established to determine the drug efficacy of BAY-876. RESULTS: A list of ubiquitination-associated signature was identified based on the screening in TCGA-BLCA cohort. Subsequent validations revealed that TRIM38 was a significant suppressor in tumors, which was expressed lowly in BLCA. Kaplan-Meier analysis and correlation analysis suggested that patients with low TRIM38 expressions had shorter survival time and advanced clinical characteristics. Targeting TRIM38 reinforced BLCA cells proliferation, migration and stemness. Mechanistically, TRIM38 interacted with GLUT1, thereby promoting its ubiquitinoylation and degradation. Furthermore, TRIM38 deficiency relied on accumulated GLUT1 proteins to enhance BLCA malignant features and cellular glycolytic capacity. We accordingly investigated the efficacy of GLUT1 inhibitor (BAY-876) in BLCA and determined its IC50 values across cell lines. Tumor xenograft models further validated that BAY-876 could effectively suppress the in vivo growth of TRIM38(low/-) BLCA. CONCLUSIONS: Our results suggested that TRIM38 plays a tumor suppressive role in BLCA pathogenesis and TRIM38/GLUT1 axis is a therapeutic vulnerability for clinical treatment, which possessing great translational significance.	bladder
Intraoperative Ventilatory Pressures During Robotic Assisted vs Open Radical Cystectomy.	OBJECTIVE: To investigate whether Robotic assisted radical cystectomy (RARC) is associated with increased postoperative pulmonary complications compared to open radical cystectomy (ORC). RARC poses challenges for ventilation with positioning and abdominal insufflation. Conventionally protective mechanical ventilation may be challenging, especially in patients with obesity or pulmonary comorbidities. Given the proven benefits of RARC compared to ORC, the risk of postoperative pulmonary complications merits further investigation. MATERIALS AND METHODS: Adult patients consented for research who underwent RARC and ORC for invasive bladder cancer from 2013-2018 were identified for retrospective chart review. Perioperative and patient variables were looked at along with postoperative course and outcomes. RESULTS: 328 patients who underwent ORC and 108 patients who underwent RARC were identified. Despite findings of higher peak airway pressures throughout surgery, patients who underwent RARC did not have a higher rate of pulmonary complications than patients who underwent ORC. Patients with obstructive sleep apnea (OSA) who underwent ORC had a higher rate of postoperative pulmonary complications. Patients who underwent RARC had a less intraoperative fluid administration, fewer ICU admissions, and decreased length of hospital stay. CONCLUSION: Despite mechanical ventilation challenges, RARC was not associated with increased post-operative pulmonary complications compared to ORC. This was also found in patients with BMI>30 or with diagnosis or high suspicion of OSA. These findings suggest ventilation at higher pressures does not increase risk for ventilator induced lung injury in patients undergoing RARC, even in conventionally higher risk patients.	bladder
Incidence and location of perioperative deep vein thrombosis in patients with bladder cancer undergoing radical cystectomy.	OBJECTIVES: To determine the incidence and location of lower extremity deep vein thrombosis in patients undergoing radical cystectomy. METHODS: We performed radical cystectomy in 137 patients with bladder cancer between August 2014 and February 2020. Since 2014, we have had a policy to screen for deep vein thrombosis using lower extremity ultrasonography both before and after radical cystectomy. We determined the incidence and location of deep vein thrombosis and classified it as either proximal or distal type. Furthermore, we explored the incidence of pulmonary embolism within 3 months after radical cystectomy. RESULTS: After excluding six patients with a lack of ultrasonographic data, we evaluated 131 patients. Preoperative deep vein thrombosis (one proximal and 17 distal) was diagnosed in 18 patients (14%) with no symptoms. Postoperative deep vein thrombosis was diagnosed in 41 patients (31%; three proximal and 38 distal), of whom 26 (63%) had new-onset deep vein thrombosis after cystectomy. Three patients, two with proximal and one with distal type deep vein thrombosis, developed nonfatal pulmonary embolism postoperatively. Multivariate analysis showed that preoperative D-dimer levels (odds ratio 5.35, 95% confidence interval 1.74-16.50; P < 0.003), type of urinary diversion (ileal neobladder; odds ratio 11.15, 95% confidence interval 2.16-57.55; P = 0.004), and preoperative deep vein thrombosis (odds ratio 15.93, 95% confidence interval 3.82-66.30; P < 0.001) were significant risk factors for postoperative deep vein thrombosis. CONCLUSIONS: Pre- and post-radical cystectomy whole-leg ultrasonography can lead to an early perioperative diagnosis and immediate treatment of proximal deep vein thrombosis, thereby potentially preventing fatal pulmonary embolism.	bladder